Unless you importing PSF+CRD, I wouldn't rely on what VMD draws to validate connectivity.
I did import the PSF+CRD, cause I don't wanted to rely on the PDB without connect records.
I believe that specifying the C1 O1 pair in both a BOND and a DOUBLE statement is redundant; I'm surprised that CHARMM does not complain about that.
Okay, the DOUBLE was just a try to see if it somehow helps, but with our without DOUBLE, the connection to O2 is missing
You may also be missing an IMPR energy term for the planarity of the carboxylate anion; the abbreviated post makes it hard to tell.
Adding "IMPR C1 C2 O2 O1" like in GLU didn't makes the O2 disappear completely.
This is really a question for the Parameter Set forum ...
Can someone move it?
Sory for the waves, I found the mistake, or at least I think so. With the toppar below I get a working PSF/CRD combination. Anyway, RMV would you mind to countercheck that toppar regarding the IMPR?This is the command sequence I used to generate the molecule:
*Test for BA
*
open read card unit 10 name top_all32_lipid_prot_cmap.rtf
read rtf card unit 10
close unit 10
open read card unit 20 name par_all32_lipid_prot_cmap.prm
read para card unit 20
close unit 20
bomlev -1
stream toppar_add_ba.str
bomlev 0
!BUILD FIRST BA MOLECULE
read sequence BA 1
generate BA setup first none last none
autogen angle dihedrals
ic param
ic seed BA 1 O1 BA 1 C1 BA 1 C2
ic build
!NBONDS CUTNB 10
hbuild
open write card unit 1 name lipids-only.psf
write psf card unit 1
open write card unit 1 name lipids-only.xplor.psf
write psf card unit 1 xplor
open write card unit 1 name lipids-only.pdb
write coor pdb unit 1
open write card unit 1 name lipids-only.cor
write coor card unit 1
stop
Please find attached the output (ba.txt) and the CRD and PSF file for BA.
Here's the full toppar:
* Toppar stream file for BA. Stream following reading of
* top_all32_lipid_prot_cmap.rtf
* and
* par_all32_lipid_prot_cmap.prm
*
read rtf card append
* BA residue
*
RESI BA -1.00 ! docosanoic acid (C22)
GROUP ! O1 O2 (-)
ATOM C1 CL 0.62 ! \\ /
ATOM O1 OCL -0.76 ! C1
ATOM O2 OCL -0.76 ! |
ATOM C2 CTL2 -0.28 ! |
ATOM H2A HAL2 0.09 ! H2A---C2---H2B
ATOM H2B HAL2 0.09 ! |
GROUP !
ATOM C3 CTL2 -0.18 ! |
ATOM H3A HAL2 0.09 ! H3A---C3---H3B
ATOM H3B HAL2 0.09 ! |
GROUP !
ATOM C4 CTL2 -0.18 ! |
ATOM H4A HAL2 0.09 ! H4A---C4---H4B
ATOM H4B HAL2 0.09 ! |
GROUP !
ATOM C5 CTL2 -0.18 ! |
ATOM H5A HAL2 0.09 ! H5A---C5---H5B
ATOM H5B HAL2 0.09 ! |
GROUP !
ATOM C6 CTL2 -0.18 ! |
ATOM H6A HAL2 0.09 ! H6A---C6---H6B
ATOM H6B HAL2 0.09 ! |
GROUP !
ATOM C7 CTL2 -0.18 ! |
ATOM H7A HAL2 0.09 ! H7A---C7---H7B
ATOM H7B HAL2 0.09 ! |
GROUP !
ATOM C8 CTL2 -0.18 ! |
ATOM H8A HAL2 0.09 ! H8A---C8---H8B
ATOM H8B HAL2 0.09 ! |
GROUP !
ATOM C9 CTL2 -0.18 ! |
ATOM H9A HAL2 0.09 ! H9A---C9---H9B
ATOM H9B HAL2 0.09 ! |
GROUP !
ATOM C10 CTL2 -0.18 ! |
ATOM H10A HAL2 0.09 ! H10A---C10---H10B
ATOM H10B HAL2 0.09 ! |
GROUP !
ATOM C11 CTL2 -0.18 ! |
ATOM H11A HAL2 0.09 ! H11A---C11--H11B
ATOM H11B HAL2 0.09 ! |
GROUP !
ATOM C12 CTL2 -0.18 ! |
ATOM H12A HAL2 0.09 ! H12A---C12--H12B
ATOM H12B HAL2 0.09 ! |
GROUP !
ATOM C13 CTL2 -0.18 ! |
ATOM H13A HAL2 0.09 ! H13A---C13--H13B
ATOM H13B HAL2 0.09 ! |
GROUP !
ATOM C14 CTL2 -0.18 ! |
ATOM H14A HAL2 0.09 ! H14A---C14--H14B
ATOM H14B HAL2 0.09 ! |
GROUP !
ATOM C15 CTL2 -0.18 ! |
ATOM H15A HAL2 0.09 ! H15A---C15--H15B
ATOM H15B HAL2 0.09 ! |
GROUP
ATOM C16 CTL2 -0.18 ! |
ATOM H16A HAL2 0.09 ! H16A---C16--H16B
ATOM H16B HAL2 0.09 ! |
GROUP !
ATOM C17 CTL2 -0.18 ! |
ATOM H17A HAL2 0.09 ! H17A---C17--H17B
ATOM H17B HAL2 0.09 ! |
GROUP !
ATOM C18 CTL2 -0.18 ! |
ATOM H18A HAL2 0.09 ! H18A---C18--H18B
ATOM H18B HAL2 0.09 ! |
GROUP !
ATOM C19 CTL2 -0.18 ! |
ATOM H19A HAL2 0.09 ! H19A---C19--H19B
ATOM H19B HAL2 0.09 ! |
GROUP !
ATOM C20 CTL2 -0.18 ! |
ATOM H20A HAL2 0.09 ! H20A---C20--H20B
ATOM H20B HAL2 0.09 ! |
GROUP !
ATOM C21 CTL2 -0.18 ! |
ATOM H21A HAL2 0.09 ! H21A---C21--H21B
ATOM H21B HAL2 0.09 ! |
GROUP !
ATOM C22 CTL3 -0.27 ! |
ATOM H22A HAL3 0.09 ! H22A---C22--H22B
ATOM H22B HAL3 0.09 ! |
ATOM H22C HAL3 0.09 ! H22C
! bonding
BOND C1 O1 C1 C2 C1 O2
BOND C2 C3 C2 H2A C2 H2B
BOND C3 C4 C3 H3A C3 H3B
BOND C4 C5 C4 H4A C4 H4B
BOND C5 C6 C5 H5A C5 H5B
BOND C6 C7 C6 H6A C6 H6B
BOND C7 C8 C7 H7A C7 H7B
BOND C8 C9 C8 H8A C8 H8B
BOND C9 C10 C9 H9A C9 H9B
BOND C10 C11 C10 H10A C10 H10B
BOND C11 C12 C11 H11A C11 H11B
BOND C12 C13 C12 H12A C12 H12B
BOND C13 C14 C13 H13A C13 H13B
BOND C14 C15 C14 H14A C14 H14B
BOND C15 C16 C15 H15A C15 H15B
BOND C16 C17 C16 H16A C16 H16B
BOND C17 C18 C17 H17A C17 H17B
BOND C18 C19 C18 H18A C18 H18B
BOND C19 C20 C19 H19A C19 H19B
BOND C20 C21 C20 H20A C20 H20B
BOND C21 C22 C21 H21A C21 H21B
BOND C22 H22C C22 H22A C22 H22B
! chain torsions
IC O1 C1 C2 C3 0.0 0.0 180.0 0.0 0.0
IC O2 C1 C2 C3 0.0 0.0 0.0 0.0 0.0
IC C1 C2 C3 C4 0.0 0.0 180.0 0.0 0.0
IC C2 C3 C4 C5 0.0 0.0 180.0 0.0 0.0
IC C3 C4 C5 C6 0.0 0.0 180.0 0.0 0.0
IC C4 C5 C6 C7 0.0 0.0 180.0 0.0 0.0
IC C5 C6 C7 C8 0.0 0.0 180.0 0.0 0.0
IC C6 C7 C8 C9 0.0 0.0 180.0 0.0 0.0
IC C7 C8 C9 C10 0.0 0.0 180.0 0.0 0.0
IC C8 C9 C10 C11 0.0 0.0 180.0 0.0 0.0
IC C9 C10 C11 C12 0.0 0.0 180.0 0.0 0.0
IC C10 C11 C12 C13 0.0 0.0 180.0 0.0 0.0
IC C11 C12 C13 C14 0.0 0.0 180.0 0.0 0.0
IC C12 C13 C14 C15 0.0 0.0 180.0 0.0 0.0
IC C13 C14 C15 C16 0.0 0.0 180.0 0.0 0.0
IC C14 C15 C16 C17 0.0 0.0 180.0 0.0 0.0
IC C15 C16 C17 C18 0.0 0.0 180.0 0.0 0.0
IC C16 C17 C18 C19 0.0 0.0 180.0 0.0 0.0
IC C17 C18 C19 C20 0.0 0.0 180.0 0.0 0.0
IC C18 C19 C20 C21 0.0 0.0 180.0 0.0 0.0
IC C19 C20 C21 C22 0.0 0.0 180.0 0.0 0.0
! impropers (from toplip.rtf ...)
IC H2A C1 *C2 C3 0.0000 0.00 120.00 0.00 0.0000
IC H2B C1 *C2 C3 0.0000 0.00 -120.00 0.00 0.0000
IC H3A C2 *C3 C4 0.0000 0.00 120.00 0.00 0.0000
IC H3B C2 *C3 C4 0.0000 0.00 -120.00 0.00 0.0000
IC H4A C3 *C4 C5 0.0000 0.00 120.00 0.00 0.0000
IC H4B C3 *C4 C5 0.0000 0.00 -120.00 0.00 0.0000
IC H5A C4 *C5 C6 0.0000 0.00 120.00 0.00 0.0000
IC H5B C4 *C5 C6 0.0000 0.00 -120.00 0.00 0.0000
IC H6A C5 *C6 C7 0.0000 0.00 120.00 0.00 0.0000
IC H6B C5 *C6 C7 0.0000 0.00 -120.00 0.00 0.0000
IC H7A C6 *C7 C8 0.0000 0.00 120.00 0.00 0.0000
IC H7B C6 *C7 C8 0.0000 0.00 -120.00 0.00 0.0000
IC H8A C7 *C8 C9 0.0000 0.00 120.00 0.00 0.0000
IC H8B C7 *C8 C9 0.0000 0.00 -120.00 0.00 0.0000
IC H9A C8 *C9 C10 0.0000 0.00 120.00 0.00 0.0000
IC H9B C8 *C9 C10 0.0000 0.00 -120.00 0.00 0.0000
IC H10A C9 *C10 C11 0.0000 0.00 120.00 0.00 0.0000
IC H10B C9 *C10 C11 0.0000 0.00 -120.00 0.00 0.0000
IC H11A C10 *C11 C12 0.0000 0.00 120.00 0.00 0.0000
IC H11B C10 *C11 C12 0.0000 0.00 -120.00 0.00 0.0000
IC H12A C11 *C12 C13 0.0000 0.00 120.00 0.00 0.0000
IC H12B C11 *C12 C13 0.0000 0.00 -120.00 0.00 0.0000
IC H13A C12 *C13 C14 0.0000 0.00 120.00 0.00 0.0000
IC H13B C12 *C13 C14 0.0000 0.00 -120.00 0.00 0.0000
IC H14A C13 *C14 C15 0.0000 0.00 120.00 0.00 0.0000
IC H14B C13 *C14 C15 0.0000 0.00 -120.00 0.00 0.0000
IC H15A C14 *C15 C16 0.0000 0.00 120.00 0.00 0.0000
IC H15B C14 *C15 C16 0.0000 0.00 -120.00 0.00 0.0000
IC H16A C15 *C16 C17 0.0000 0.00 120.00 0.00 0.0000
IC H16B C15 *C16 C17 0.0000 0.00 -120.00 0.00 0.0000
IC H17A C16 *C17 C18 0.0000 0.00 120.00 0.00 0.0000
IC H17B C16 *C17 C18 0.0000 0.00 -120.00 0.00 0.0000
IC H18A C17 *C18 C19 0.0000 0.00 120.00 0.00 0.0000
IC H18B C17 *C18 C19 0.0000 0.00 -120.00 0.00 0.0000
IC H19A C18 *C19 C20 0.0000 0.00 120.00 0.00 0.0000
IC H19B C18 *C19 C20 0.0000 0.00 -120.00 0.00 0.0000
IC H20A C19 *C20 C21 0.0000 0.00 120.00 0.00 0.0000
IC H20B C19 *C20 C21 0.0000 0.00 -120.00 0.00 0.0000
IC H21A C20 *C21 C22 0.0000 0.00 120.00 0.00 0.0000
IC H21B C20 *C21 C22 0.0000 0.00 -120.00 0.00 0.0000
IC C20 C21 C22 H22A 0.0000 0.00 180.00 0.00 0.0000
IC H22A C21 *C22 H22B 0.0000 0.00 120.00 0.00 0.0000
IC H22A C21 *C22 H22C 0.0000 0.00 -120.00 0.00 0.0000
end
return